Twins manager Rocco Baldelli was suspended one game. Duffey and Baldelli also were fined undisclosed amounts.
Major League Baseball announced the suspensions two days after Duffey threw the pitch in apparent retaliation for Mercedes' controversial home run off a 3-0 pitch in a blowout victory Monday.
Duffey elected to appeal his suspension and pitched in the first game of Thursday's doubleheader against the Los Angeles Angels. He gave up four hits and three runs in the fifth inning of Minnesota's 7-1 loss. Baldelli served his one-game ban in the second game, a 6-3 Twins victory.
White Sox manager Tony La Russa criticized his own player for the swing, calling it a "big mistake" and saying Mercedes was "just clueless" for not being aware of baseball's unwritten rules. Baldelli also expressed his disappointment before Tuesday's game -- and Duffey took matters into his own hands in the seventh inning when he threw a pitch behind Mercedes.
Minnesota rallied for a 5-4 victory Tuesday, and La Russa said after the game that he "didn't have a problem with how the Twins handled that."
Mercedes, a 28-year-old rookie, entered Thursday with a majors-leading .358 average and has six homers and 25 RBIs this season.